The fast-casual restaurant's stock plunged Friday after the Centers for Disease Control and Prevention reported that the E.coli outbreak hindering the company had widened to a total of six states. Still, Chipotle shares were up 5 percent late morning Monday.

"People are trying to factor in [the price fall]," Cramer said. "My problem is that, we don't know what the duration [will be]; we don't know if they have a handle on it.

Nonetheless, Cramer added he thinks Chipotle will be able to move past this." They are responsible people who will get to the bottom of it, and when they do, I think we will say 'wow, that's past them.'"

DISCLOSURE: Cramer's trust did not own Chipotle's stock when this article was published.